A Nefarious Matter
by Shadougelover14
Summary: Set after A4O. Ratchet and Clank are getting suspicious when they don't hear from Nefarious for a while, so they decide to investigate. Meanwhile, Nefarious is having issues of his own... BTW, happy late b-day Neffy!  Mar. 9!
1. Chapter 1

A large armored ship was moving through space. Inside, dozens of troops flew about, welding things here, organizing things there. On the finished half of the ship was a large office. It had large windows that looked out into space, a shelf stacked with books, and a long desk with a hover chair behind it.

It was in this chair that a certain android was sitting, his head resting on the table with an arm over it as another robot in the room was giving him the latest details about the station.

"Another few days, and the space station should be completed. After that we'll install the weapons and defense systems." Lawrence announced.

"Splendid…" Nefarious muttered.

"We'll be putting in those new dark matter energy rays you built. I'm sure they'll pack quite a punch."

"Wonderful…"

"And the computers are going over those diagrams of those guardian bots you scanned. We could start building some of those if you'd like."

Nefarious merely grunted in reply this time. Lawrence glanced at him.

"Something wrong sir?"

"No, everything's fine…"

Lawrence wasn't buying it.

"Is there anything in particular you would like for me to install? Or if there's something you didn't like-"

"I'm fine okay!" Nefarious growled. This only proved Lawrence's theory.

"This wouldn't happen to be about Magnus would it?" he asked.

"NO!" Nefarious shouted, jumping to his feet in anger. A few seconds passed as Lawrence gave him a skeptical look.

"…Yes…" Nefarious sighed, slumping back down in his chair as he crossed his arms.

"Don't let it keep bothering you sir, you said so yourself. The only reason you helped out Ratchet and his friends was to get back home."

"Right…" Nefarious mumbled as he tapped one of his claws on the table idly.

Lawrence sighed as he tried to think of something that would make Nefarious' mood lift.

"Would you like for me to gather some of the troops for you to practice your space opera with?"

"No…just get me some coffee or something…" Nefarious replied as he twisted the chair around to face the window.

Lawrence sighed as he turned and walked towards the door.

"Anything in particular you would like in it?"

"I don't care…"

Lawrence left the room, and the door closed behind him. Nefarious glanced at the door, before repositioning himself so he was sitting side ways in the chair with one foot resting against the arm of the chair and his other leg hanging over the side, while his arms rested on stomach.

After a few minutes, he glanced at a locked drawer in his desk, before glancing away and glaring at the ceiling.

'_Don't do it! Don't even think about it!'_ he growled in his mind.

A minute later, he was unlocking the drawer and removing the item inside. It was a picture of himself, along with Ratchet, Clank, and Qwark, just before they left Magnus- or actually, before Nefarious had swiped their ship and abandoned them on the floating rock.

He hadn't felt too guilty about it, he knew they'd find another way off; they always had a way of evading disaster.

What was troubling him was the fact he felt even a splinter of guilt at all. He was Dr. Nefarious! The most notorious, diabolical super villain this universe had ever known! He shouldn't feel guilty about anything!

And yet…he did.

He hated to admit it, really, REALLY hated it, but he'd actually sort of enjoyed working with Ratchet and his friends. They'd actually made a pretty good team too…

Nefarious shook his head roughly. No! He couldn't think like that! Emotions were for squishies! He shoved the photo back in the drawer and locked it.

He sighed as he leaned back in the chair, trying to sort things in his head. There had to be some way to figure this all out…

"Sir?" a voice suddenly spoke from behind.

Nefarious yelped as he jumped forward, slamming into the window, and sliding to the floor. He stood, quickly regaining his composure, and turned around to face Lawrence with an annoyed expression.

"What is it, Lawrence? This better be important!"

"I was merely going to make a suggestion. Perhaps you should speak to a therapist." Lawrence suggested as he set a cup of coffee on the desk.

"I don't need therapy!"

"Sir, if I may, you have been acting rather strangely ever since we got back from Magnus. The best thing to do would be to talk about it so it's not clouding up your mind."

Nefarious glaring at him, but there was a hint of uncertainty. Then he smirked.

"Alright then, Lawrence, if you think it's such a good idea, then _you_ can be my therapist!"

Lawrence sighed; he'd had a pretty good idea this would happen.

'_Oh goodie, as if I don't hear him complain enough…'_ he thought.

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This'll be a short story, 3 or 4 chapters, taking place after A4O. Spoiler Alert! The final cut scene kinda got me thinking Nefarious will have a change of heart, seeing as he was close to tears when looking at that picture. Anyway, leave a review please!


	2. Chapter 2

Ratchet and Clank were on the Phoenix, relaxing after their most recent adventure on Magnus.

"That was some trip, eh Clank?"

"You can say that again. I haven't had that much excitement since we had to defeat Nefarious at the Great Clock."

"Yeah, only a little freakier. Seriously, that squirrel thing when it was possessed was scary."

"Speaking of Nefarious, don't you find it a bit odd we haven't had any problems with him for a while now?"

"Well, maybe he's thinking up some dramatic attack to thank us for helping him out."

"Ratchet, it's been two weeks without some sort of attack. He hasn't even sent another death threat to Qwark."

Almost immediately, the green clad president appeared.

"Hey, I thought I heard my name. Discussing your favorite super hero/loved president, right? I have pictures for autographs." Qwark announced, holding up a stack of photos.

Ratchet sighed. "No thanks, Qwark. I still have the signed photo from yesterday."

"Oh," Qwark tossed the photos over his shoulder and sat in another chair beside the duo, "So, what's the wanna be hero Lombax and his sidekick doing today?"

"Oh nothing, Clank's worried about the fact we've had two sweet weeks of relaxation without Nefarious launching an attack on us."

"You know I have been wondering about that guy."

"Maybe we should pay him a visit." Clank suggested.

"Uh, hello, this is Nefarious we're talking about. The second we get within 50 feet of that space station we heard about, he'll try to 'ANNIALATE US!'." Ratchet stated, copying Nefarious' favorite saying.

"Ratchet, surely you're concerned as well."

"Well...yeah, but, I mean, what can we say? 'Oh hey, Nefarious, haven't heard from ya in two weeks, just wanted to make sure you're not planning any dominations or revenge plots.'"

"I'm sure we'll think of something."

Ratchet and Clank stared at one another for a minute, before the Lombax sighed.

"Alright, guess we're goin'."

"Not so fast cadets, this will be dangerous. What you need is a strong, handsome, brilliant natural leader. Luckily for you, you know one of those." Qwark stated.

"Uh, Qwark, that's okay, we can handle this on our own."

"Nonsense, you wouldn't last 5 minutes."

Ratchet shook his head, before smirking.

"Hey Qwark, you wouldn't happen to have any action figures would you?"

"Why yes I do! There in my room, wanna see?"

Qwark ran off before anyone could answer.

"Alright, let's leave before he comes back." Ratchet said.

Clank nodded, and the duo quickly made their way towards where their ship was held.

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"Alright, so, how are we gonna find his space station?" Ratchet asked.

"Look for his signal." Clank replied simply, punching something into the tracker.

"Clank, come on, he may be a few chips shy of a mother board, but even he wouldn't make himself that easy to find-"

Ratchet paused when the tracker pinged, and a dot appeared.

"Or you know, maybe he would. Aphelia, can you go to that location?"

"You got it." Aphelia replied.

The ship took to the air, and flew off in a burst of speed.

Meanwhile, Qwark returned to the room with a large load of action figures.

"Alright guys, I got all kinds of action figures, so just pick one and I'll happily sign it for-" he paused when he realized they were gone.

"Huh? Hey, where'd everybody go?" he wondered aloud as he looked around.

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Sorry it's short. Next one will be a little longer I promise.


	3. Chapter 3

"For the record, this was your idea." Ratchet panted as he destroyed another of Nefarious' troops.

"I know." Clank replied.

Finally, they cleared the hall, and continued on.

"I guess I can understand why Nefarious has been so quiet. He musta been finishing up this place. He's gotta keep his plans around here somewhere…" Ratchet said.

After about 5 minutes, they came to a large door.

"If I were an evil mad scientist, this is where I would keep all my evil plans." Ratchet stated.

"We should proceed with caution." Clank added.

Ratchet nodded, and they faced the door. He gripped his wrench tightly, then charged at the door. He threw one of his bombs at it, and it blew open, filling the air with smoke and debris. They charged into the room before hearing a loud shriek.

::::

Nefarious and Lawrence had been in the doctor's office. Nefarious was lying on a couch, while Lawrence was in a lazy chair, holding a clipboard and scribbling something down.

Suddenly, the door blew in, startling them both. Nefarious screeched as he leapt into the air, before being caught by Lawrence. Ratchet and Clank ran into the room.

Both parties were staring at each other, before Lawrence and Nefarious became aware of their awkward position. The butler hurriedly dropped the doctor, who hit the floor with a metallic thud, before scrambling to his feet.

"Seems we'll have to replace the door." Lawrence sighed.

"What was that for?" Nefarious exclaimed angrily as he stalked over to the duo.

"Er, stopping your evil plotting?" Ratchet stated questioningly.

"Evil plot- WHAT EVIL PLOTTING?"

"Isn't that what you're usually doing?"

"I have other things to do besides that! Like building a new space station, and now I have to find new doors!"

"Er, sorry?"

"If you're not scheming, what are you doing?" Clank asked.

"We were in the middle of a therapy session-" Lawrence started, before being interrupted by Nefarious.

"No we weren't!"

"Nefarious needs therapy? What a surprise…" Ratchet muttered. The doctor was glaring at him, before storming out of the room.

"So, what's his problem?"

"I'm afraid I can't tell you that. Patient confidentiality you know." Lawrence replied, putting a manila folder in a filing cabinet and locking it.

"Now if you'll excuse me, I have _many_ things to do. I probably won't be in here for a while…" he stated, setting the key to the drawer on the desk and headed for the entry way.

After he left, Ratchet glanced at the desk where the key lay. He walked over, took it, and opened the drawer.

"Ratchet, didn't he say it was private?" Clank asked.

"If it was he wouldn't have left the key where we could get to it," Ratchet replied as he pulled out the folder, "Besides, don't tell me you don't wanna look at Nefarious' records."

Clank paused for a moment, before walking over, and Ratchet opened the folder.

"Let's see. Name, biography, past achievements…wow that's a small section…and, here we go, problem. Let's see…"

Ratchet read over the things Lawrence had written down.

"Whoa."

"What is it?" Clank asked.

"It says that Nefarious has been having guilt issues."

"Dr. Nefarious? Feel guilty?"

"Yeah, about leaving us on Magnus. It also says he can't figure out why he cares, or why he feels bad for leaving us."

"Hm, that doesn't sound like the Nefarious we know."

"Lawrence put something else. It says, solution: have Lombax and his sidekick talk to him. Wait, _what_?"

"Perhaps Lawrence meant for us to find this."

"What are we supposed to do?"

"I'm not sure, but I think our best first step would be to find him."

"Okay, so, where would we find him? This station's huge, he could be anywhere."

A small slip of paper fell out of the folder, along with a photo. Ratchet picked up the picture while Clank got the paper.

"We could try here." He stated, showing Ratchet the paper, which had a note on it.

"From the office, 3rd hall on the right, and first door on the left. Alright, guess we're going to be therapists, let's go." Ratchet sighed.

"What else fell out?"

"Oh, it's that picture we took before we left Magnus."

It had the four of them together, all looking pretty happy, even Nefarious.

"He did seem different after the whole thing, ya know, before he stole our ship and abandoned us." Ratchet remarked.

"I still think we should try Ratchet, I do believe there might be some good in him."

"Yeah, just don't let him hear ya say that."

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So, how was that? Hope you liked, leave a comment please!


	4. Chapter 4

"Nefarious?" Ratchet called as he and Clank walked into the room they'd been directed to.

There was no sign of the doctor anywhere, and as they ventured in further, they took in the room. There were tools, metal tables, and boards with blue prints tacked on all over the place.

"Nice place…" Ratchet remarked as he looked around.

"This is probably where Dr. Nefarious builds his robots." Clank stated.

Ratchet nodded, before pausing. Clank did similarly, and they could hear grumbling from somewhere further in the large room.

The ventured further, and saw Nefarious up ahead with his back to them, leaning on a table that was covered with various sheets of paper.

"Blowing up MY doors…butting into MY business…I outta annihilate them while they're still here…"

"Um, Nefarious?" Ratchet called.

The doctor yelped and whipped around, slipping on a pencil that had fallen to the floor and hitting the back of his head on the table. He dazedly lifted his head, and glared at them as soon as they came into view.

"What the heck are _YOU _doing in here? Wait, _how _the heck did you even _find_ here?" he shouted as he stood.

"Umm, we…followed you?" Ratchet replied nervously.

"No, Lawrence gave us directions." Clank stated.

Ratchet sighed as he pinched his eyebrows together. "We weren't supposed to tell him that…"

"LAAAAAAWREE-" Nefarious shouted furiously at the top of his metaphorical lungs.

"_Oh Lance! I've been lying to you! My name's not really Janice! It's Clarabelle!" _

"_It's okay, Clarabelle! My name's not really Lance! It's Bob!"_

"_Oh Bob!"_

"_Oh Clarabelle!"_

"Oh brother…" Ratchet sighed, before picking up a good sized wrench and throwing it at Nefarious' head.

"-EEEEEEENCE!"

Elsewhere in the ship, Lawrence heard the shout, and sighed.

"So much for secrecy…"

"So, what's been eatin' you? You haven't tried taking over the universe or killing Qwark in a while." Ratchet asked.

"Nothing alright! Just get out of here!"

"That's not what your file said."

Nefarious paused for a second, and Clank took the moment to speak up.

"You feel guilty about leaving us on Magnus, correct?"

"…"

"We read the file through, so we know everything."

Nefarious grumbled under his breath, and the duo heard 'I'm gonna KILL him' somewhere in there.

"It helps to-"

"Talk, I know! Lawrence already said that! Twice!"

"So…talk." Ratchet said.

Nefarious froze again, before glancing away for a second. Finally, he turned away and crossed his arms, mumbling something.

"Sorry, come again?"

"I said I'm…." Nefarious mumbled quietly.

"What?"

"I'M SORRY OKAY?" Nefarious shouted, whipping around and glaring at them.

A minute passed in total silence, except for the whirring of the ship and the gears in Nefarious' head and body.

"You're…sorry?" Ratchet finally asked.

"Do NOT make me repeat that!"

"You, Dr. Nefarious, scourge of the universe, hater of all organic life, are apologizing?"

"Do you want a gift basket? Yes, alright, I'm apologizing! Can we get past that?"

"But I thought you hated us." Clank stated.

"I did! I mean I do! I mean…"

Nefarious trailed off, before turning away.

Ratchet and Clank looked at each other, before looking back the robotic doctor.

"So when exactly did you stop hating us?" Ratchet asked.

Nefarious turned back with a glare, opening his mouth to shout a denial, but upon seeing the knowing looks on the duo's faces, paused, and glanced away.

"…..It kind of just…fizzled out after we started working together…."

"You were pretty helpful ya know. You found Ephemeris' charging dock, and not to mention you saved Qwark."

At this Nefarious shuddered.

"PLEASE don't remind me…"

Ratchet snickered, before continuing.

"If you were starting to like us, why'd you take our ride?"

"Well…I figured I'd get…tossed in jail or something, ya know? I _did_ attack Luminopolis with a Z'Grute and nearly destroyed the city, remember?"

"Yeah, but I bet if you'd stuck around, Qwark woulda pardoned you, and we would've explained things to Kronk and Zephyr. To put it simply, we might've actually been friends."

"Friends? Friends…remind me what that is again?"

The duo just stared at him.

"You don't know what a friend is?" Ratchet asked incredulously.

Nefarious merely blinked, awaiting an answer.

"Well, a friend is…well, a friend's like Clank. Always by my side, helping me, even telling me off when I need it."

"For you, a good comparison would be Lawrence." Clank stated, before being interrupted.

"We're not friends! Associates would be a better word!" Nefarious retorted.

"Anyway, as I was saying, Lawrence has stuck by you despite everything, probably rebuilt you dozens of times, and most recently tried to help you sort out your emotional issues."

"Yes, well…I suppose strong acquaintanceship could work…"

"Oh face it, you're friends and you know it-"

Ratchet was cut off by a loud shout.

"Greetings cadets and mad scientists!"

The trio yelped and glanced around. Qwark was standing behind Ratchet and Clank, and Lawrence was behind him.

"Dreadfully sorry sir, I attempted to keep him out. I'm not even sure how he found this room." The butler stated.

"Easy, I just followed the directions on this piece of paper I found. Oh, by the way, Ratchet, here's that action figure you wanted. I went to my room to get it, but when I came back you were gone. You must've forgotten." Qwark stated as he handed the Lombax an action figure of himself in a heroic, yet goofy, stance.

"Thanks Qwark, how could I have forgotten?" Ratchet muttered as he glanced at the doll.

"So, having guilt issues, eh? I've been there once-"

"NO I'M NOT! How do you even know about-"

Nefarious cut himself off, and glared at Lawrence. The robotic butler raised his hands in surrender.

"I didn't say a word."

"No, it was all in this neat little file somebody left on your desk." Qwark stated.

At this, _everybody_ turned a glare to Ratchet. He put his hands behind his back and whistled innocently.

"Anyway, I've got the solution to your problem: game night!" Qwark announced.

"…What?"

"It's a night where the Q-Force plays video games." Ratchet stated.

"It's super riveting and chock full of excitement! Plus I kick everyone's butt every time." Qwark added.

"That's because you cheat and knock everyone out with sleeping gas."

"Wait there's cheating involved? I mean, I DON'T CARE!" Nefarious shouted.

"Come on, Doc, it'll be fun!" Qwark didn't wait for an answer, and grabbed Nefarious' arm and yanked him out the door. The others could hear him shouting down the hall.

"GET YOUR SQUISHIE HANDS OFF OF ME! UNHAND ME BEFORE I RIP YOU APART! LAWREEENCE!"

"Okay…" Ratchet said.

"I think that went rather well." Lawrence stated.

"So, why did you have us talk to him?" Clank asked.

"I obviously couldn't get through to him. So I got the next best people; the ones who are causing his dilemma."

"Who'd of thought Nefarious would feel guilty about anything?" Ratchet asked.

"Yes, it is rather surprising. I think it's all due to the fact he used to be organic himself."

"Perhaps our trip to Magnus and experiencing the benefits of having friends helped with that." Clank stated.

"You make it sound so complicated. We banded together, saved the universe, and became friends, simple as that." Ratchet sighed.

Suddenly Qwark popped back in.

"Hey Lawrence, you should come too it'll be fun!"

"Where's Nefarious?" Ratchet asked.

"Oh, he froze up in mid shout again. Let's go, and hurry! He's playing the final episode of Lance and Janice! It's the one where Janice reveals her big secret!"

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"I'd say game night is going surprisingly well. Ya know, after we kept everyone from pummeling Lawrence and Nefarious." Ratchet stated as he and Clank watched Qwark fighting Skidd over a controller.

Nefarious was sitting Indian style on the couch furthest away from the group, glaring at nothing in particular. Lawrence stood beside the couch, also watching the fight.

"Come on, Doc, you should play, it'll be fun!" Qwark remarked.

"Just because you glued the controller to my hands doesn't mean I'm going to play!" Nefarious growled as he held up his hands, which were glued to a controller.

"Fine…"

While Qwark continued his argument with Skidd, Nefarious once again attempted to get the controller off with his foot.

"Stupid thing! Help me, Lawrence!" he grumbled.

Lawrence started pulling while Nefarious pushed on the controller with his foot, and Ratchet couldn't help but laugh at the scene.

"Silence squishie! This isn't funny!"

"Are you kidding, it's hilarious."

"If my hands weren't glued to this, I'd- AAAAGH!"

Nefarious had stood from the couch, but tripped over the cord for the controller. Everyone burst out laughing, while Nefarious growled to himself.

"Wow Doc, you're easier to trip in real life than the game." Qwark remarked as his video game persona socked Nefarious' to the ground.

Nefarious' eye twitched, and the controller suddenly exploded as dark energy formed in his hands.

"Here's a fun game for ya!" he growled as he made to throw an energy blast at Qwark.

"Whoa, whoa, okay, cool the dark matter." Ratchet ordered as he and Lawrence held him back.

"Do relax sir."

Nefarious yanked free and plopped down on the couch, grumbling to himself. Cronk and Zephyr pulled Ratchet aside.

"Are ya sure about him, rookie?" Cronk asked as he cast a suspicious look at Nefarious.

"Totally. Sure he's a little short tempered, but given his reasons, it's understandable. Qwark can annoy anybody." Ratchet replied.

"True. Well, I guess we can just overlook things. But if he tries anything, I'm watching the little whippersnapper!"

"Heh, you do that."

They returned to the group, where Qwark was still trying to convince Nefarious to play.

"Come on Doc, it's fun!"

"No! I don't do fun!"

"You're just afraid I'll beat you!"

"Please! I can kick your butt at anything! Including intelligence…"

Qwark paused, before smirking.

"Fine, I guess if you're too afraid to play. The controls _are_ tricky after all."

At this, Nefarious perked up.

"Tricky is good. _Tricky_ I can do. Give me that!" he swiped a controller from Clank.

Ratchet snickered, and kicked back with a soda while Nefarious and Qwark's characters went at each other, and the duo was shouting at each other while the others cheered them on.

'_I guess having Nefarious around won't be so bad. It'll definantly make things interesting…'_ he thought with a sigh.

Angered shouts sounded from Nefarious and Qwark as they claimed the other had cheated, before quickly denying the other's claim.

"Calm down everyone!" Sasha yelled.

"He started it!" Nefarious and Qwark yelled in unison, and turned on each other.

"I did not, you did!"

"Here we go." Lawrence sighed.

"Eh, I'm sure they'll get along better…eventually." Ratchet remarked.

Lawrence merely shook his head, and the duo watched as Nefarious and Qwark continued their argument.

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Well, that's the end of this story. Hope you enjoyed! R&R!


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